Towards an HLA Run-time Infrastructure with Hard Real-time Capabilities

Our work takes place in the context of the HLA standard and its application in real-time systems context. The HLA standard is inadequate for taking into consideration the different constraints involved in real-time computer systems. Many works have been invested in order to providing real-time capabilities to Run Time Infrastructures (RTI) to run real time simulation. Most of these initiatives focus on major issues including QoS guarantee, Worst Case Transit Time (WCTT) knowledge and scheduling services provided by the underlying operating systems. Even if our ultimate objective is to achieve real-time capabilities for distributed HLA federations executions, this paper describes a preliminary work focusing on achieving hard real-time properties for HLA federations running on a single computer under Linux operating systems. Our paper proposes a novel global bottom up approach for designing real-time Run time Infrastructures and a formal model for validation of uni processor to (then) distributed real-time simulation with CERTI

Real-Time Distributed Aircraft Simulation through HLA

This paper presents some ongoing researches carried out in the context of the PRISE (Research Platform for Embedded Systems Engineering) Project. This platform has been designed to evaluate and validate new embedded system concepts and techniques through a special hardware and software environment. Since many actual embedded equipments are not available, their corresponding behavior is simulated using the HLA architecture, an IEEE standard for distributed simulation, and a Run-time infrastructure called CERTI and developed at ONERA. HLA is currently largely used in many simulation applications, but the limited performances of the RTIs raises doubts over the feasibility of HLA federations with real-time requirements. This paper addresses the problem of achieving real-time performances with HLA. Several experiments are discussed using well-known aircraft simulators such as the Microsoft Flight Simulator, FlightGear, and X-plane connected with the CERTI Run-time Infrastructure. The added value of these activities is to demonstrate that according to a set of innovative solutions, HLA is well suited to achieve hard real time constraints

Clinical application of high throughput molecular screening techniques for pharmacogenomics.

Genetic analysis is one of the fastest-growing areas of clinical diagnostics. Fortunately, as our knowledge of clinically relevant genetic variants rapidly expands, so does our ability to detect these variants in patient samples. Increasing demand for genetic information may necessitate the use of high throughput diagnostic methods as part of clinically validated testing. Here we provide a general overview of our current and near-future abilities to perform large-scale genetic testing in the clinical laboratory. First we review in detail molecular methods used for high throughput mutation detection, including techniques able to monitor thousands of genetic variants for a single patient or to genotype a single genetic variant for thousands of patients simultaneously. These methods are analyzed in the context of pharmacogenomic testing in the clinical laboratories, with a focus on tests that are currently validated as well as those that hold strong promise for widespread clinical application in the near future. We further discuss the unique economic and clinical challenges posed by pharmacogenomic markers. Our ability to detect genetic variants frequently outstrips our ability to accurately interpret them in a clinical context, carrying implications both for test development and introduction into patient management algorithms. These complexities must be taken into account prior to the introduction of any pharmacogenomic biomarker into routine clinical testing

PRISE: An Integrated Platform for Research and Teaching of Critical Embedded Systems

In this paper, we present PRISE, an integrated workbench for Research and Teaching of critical embedded systems at ISAE, the French Institute for Space and Aeronautics Engineering. PRISE is built around state-of-the-art technologies for the engineering of space and avionics systems used in Space and Avionics domain. It aims at demonstrating key aspects of critical, real-time, embedded systems used in the transport industry, but also validating new scientific contributions for the engineering of software functions. PRISE combines embedded and simulation platforms, and modeling tools. This platform is available for both research and teaching. Being built around widely used commercial and open source software; PRISE aims at being a reference platform for our teaching and research activities at ISAE

An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs.

Reconstructing full-length transcript isoforms from sequence fragments (such as ESTs) is a major interest and challenge for bioinformatic analysis of pre-mRNA alternative splicing. This problem has been formulated as finding traversals across the splice graph, which is a directed acyclic graph (DAG) representation of gene structure and alternative splicing. In this manuscript we introduce a probabilistic formulation of the isoform reconstruction problem, and provide an expectation-maximization (EM) algorithm for its maximum likelihood solution. Using a series of simulated data and expressed sequences from real human genes, we demonstrate that our EM algorithm can correctly handle various situations of fragmentation and coupling in the input data. Our work establishes a general probabilistic framework for splice graph-based reconstructions of full-length isoforms

Distributed Simulation of Heterogeneous and Real-time Systems

This work describes a framework for distributed simulation of cyber-physical systems (CPS). Modern CPS comprise large numbers of heterogeneous components, typically designed in very different tools and languages that are not or not easily composeable. Evaluating such large systems requires tools that integrate all components in a systematic, well-defined manner. This work leverages existing frameworks to facilitate the integration offers validation by simulation. A framework for distributed simulation is the IEEE High-Level Architecture (HLA) compliant tool CERTI, which provides the infrastructure for co-simulation of models in various simulation environments as well as hardware components. We use CERTI in combination with Ptolemy II, an environment for modeling and simulating heterogeneous systems. In particular, we focus on models of a CPS, including the physical dynamics of a plant, the software that controls the plant, and the network that enables the communication between controllers. We describe the Ptolemy extensions for the interaction with HLA and demonstrate the approach on a flight control system simulation

Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining

MHC (Major Histocompatibility Complex) is a key player in the immune response of an organism. It is important to be able to predict which antigenic peptides will bind to a spe-cific MHC allele and which will not, creating possibilities for controlling immune response and for the applications of immunotherapy. However a problem encountered in the computational binding prediction methods for MHC class I is the presence of bulges and loops in the peptides, changing the total length. Most machine learning methods in use to-day require the sequences to be of same length to success-fully mine the binding motifs. We propose the use of time-based data mining methods in motif mining to be able to mine motifs position-independently. Also, the information for both binding and non-binding peptides are used on the contrary to the other methods which only rely on binding peptides. The prediction results are between 70-80% for the tested alleles

Densifying the sparse cloud SimSaaS: The need of a synergy among agent-directed simulation, SimSaaS and HLA

Modelling & Simulation (M&S) is broadly used in real scenarios where making physical modifications could be highly expensive. With the so-called Simulation Software-as-a-Service (SimSaaS), researchers could take advantage of the huge amount of resource that cloud computing provides. Even so, studying and analysing a problem through simulation may need several simulation tools, hence raising interoperability issues. Having this in mind, IEEE developed a standard for interoperability among simulators named High Level Architecture (HLA). Moreover, the multi-agent system approach has become recognised as a convenient approach for modelling and simulating complex systems. Despite all the recent works and acceptance of these technologies, there is still a great lack of work regarding synergies among them. This paper shows by means of a literature review this lack of work or, in other words, the sparse Cloud SimSaaS. The literature review and the resulting taxonomy are the main contributions of this paper, as they provide a research agenda illustrating future research opportunities and trends